How to compute DS (diploid dosage) from HDS (haploid dosage) in VCF?

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Assessment

Difficulty
3/5
Estimated time
1-2 days
Newbie friendliness
25/100
Issue type
Documentation
Clarity
Needs clarification
Activity status
Stale
Domain
bioinformatics, cli

Research direction

Start with the issue's GT:HDS example and VCF header snippet, then inspect the bcftools command and plugin documentation for dosage transformations. Done means establishing whether an existing command or plugin supports this conversion and documenting the applicable guidance or limitation.

Written by the indexing model from the issue text.

Description

needs-feedback

Hello,
I have a VCF file with GT:HDS (haploid dosage) values, but I need to generate GT:DS (diploid dosage), since this is the most common format in vcf files and used commonly for association analyses.

Is there a bcftools command or plugin to compute or convert the GT:DS field from GT:HDS?

The VCF FORMAT column is GT:HDS. A sample line looks like:
chr22 10510303 ... GT:HDS 0|0:0,0 0|0:0.001,0 ...

VCF Header Snippet:
##FORMAT=<ID=HDS,Number=2,Type=Float,Description="Haploid Alternate Allele Dosage">

Thank you in advance for your guidance.

Dominant language
C
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Merged PRs (30d)
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